What is my best option, re install Buddypress and start again ( OUCH! many weeks of work in my free time) or is there a smart way of re instating the members directory. I am guessing the members data is lost even though the members id is still intact as are the avatars.

Well WP Super Cache is not very compatible with BP sites. Now that your .htaccess has changed, try logging into the dashboard and going to settings > permalinks, then resave your permalinks settings. This will set your .htaccess to work correctly with pretty permalinks again. Hopefully, that fixes the issue.

Bump with and update in the hope that anyone has seen this before or have any ideas.

If I turn off extended profiles in BP component admin I can access the basic profile from both the avatar link and the BP nav bat. It is only with extended profiles enable that I see the error. Could this be a directory problem?